I actually don't know the significance of using 2.  This was another reason I was getting different read counts vs GATK as their default min base quality is 6.  At least this way its parameterizable, but if there is a more justified default we should probably change it to that.  Or add a command line argument for it.

On that note, the argument options for Transform are growing large - is the goal to keep all of the operations in there (and all their various configurations) or to start splitting them out?